Hi,
I am still relatively new to PyRosetta so excuse my ignorance if the answer to this question is obvious.
I would like to do protein design calculations and the material I have read uses PackRotamersMover. I'm having no problems running these calculations. But I am not sure how to do some minor minimization of the structure after each design move when I apply PackRotamersMover. So when the algorithm outputs at the end that it built X rotamers at Y positions, I would like for it to have done X minimizations too.
Any help with this matter is much appreciated.
Troy Wymore
Post Situation:
You're looking for the MinPacker (see protocols.simple_moves.MinPackMover for the friendliest interface). It works exactly like the PackRotamersMover, except that every time it considers a rotamer, it minimizes it first. (It does this throughout the simulated annealing, though, not during the initial build, as minimization will be context dependent.)
Thanks so much for the advice. Here is the list of commands that I used in case it can help someone else.
In [1]: from rosetta import *
In [2]: rosetta.init()
In [3]: pose = pose_from_pdb("filename.pdb")
In [4]: scorefxn = create_score_function("standard")
In [5]: print scorefxn(pose)
In [6]: task = TaskFactory()
In [7]: task.push_back(InitializeFromCommandline())
In [8]: task.push_back(ReadResfile("filename.resfile"))
In [9]: s_mover = SequenceMover()
In [10]: design_mover = MinPackMover()
In [11]: design_mover.task_factory(task)
In [12]: design_mover.score_function(scorefxn)
In [13]: s_mover.add_mover(design_mover)
In [14]: s_mover.apply(pose)
In [15]: print pose.residue(90).name()
SER
In [16]: print pose.residue(135).name()
VAL
In [17]: scorefxn.show(pose)
In [18]: pose.dump_pdb("filename-redesign.pdb")